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- PDB-6b4k: Crystal structure of human DDX19B(AMPPNP) -

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Basic information

Entry
Database: PDB / ID: 6b4k
TitleCrystal structure of human DDX19B(AMPPNP)
ComponentsATP-dependent RNA helicase DDX19B
KeywordsTRANSPORT PROTEIN / Complex / Nuclear Pore Complex / mRNA export / DEAD-box helicase
Function / homology
Function and homology information


poly(A)+ mRNA export from nucleus / mRNA export from nucleus / nuclear pore / helicase activity / cytoplasmic stress granule / nuclear envelope / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity ...poly(A)+ mRNA export from nucleus / mRNA export from nucleus / nuclear pore / helicase activity / cytoplasmic stress granule / nuclear envelope / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal ...RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / MALONATE ION / ATP-dependent RNA helicase DDX19B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLin, D.H. / Correia, A.R. / Cai, S.W. / Huber, F.M. / Jette, C.A. / Hoelz, A.
CitationJournal: Nat Commun / Year: 2018
Title: Structural and functional analysis of mRNA export regulation by the nuclear pore complex.
Authors: Lin, D.H. / Correia, A.R. / Cai, S.W. / Huber, F.M. / Jette, C.A. / Hoelz, A.
History
DepositionSep 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DDX19B
B: ATP-dependent RNA helicase DDX19B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6839
Polymers97,3162
Non-polymers1,3677
Water3,873215
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A: ATP-dependent RNA helicase DDX19B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3935
Polymers48,6581
Non-polymers7354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent RNA helicase DDX19B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2914
Polymers48,6581
Non-polymers6333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.233, 45.364, 127.391
Angle α, β, γ (deg.)90.00, 97.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP-dependent RNA helicase DDX19B / DEAD box RNA helicase DEAD5 / DEAD box protein 19B


Mass: 48658.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX19B, DBP5, DDX19, TDBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UMR2, RNA helicase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MIB buffer pH 5.0 (malonate, imidazole, borate), 13 % (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 48313 / % possible obs: 99.4 % / Redundancy: 6.9 % / CC1/2: 0.994 / Rpim(I) all: 0.053 / Rsym value: 0.14 / Net I/σ(I): 10
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4099 / CC1/2: 0.452 / Rpim(I) all: 0.979 / Rsym value: 2.456 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EWS

3ews


Resolution: 2.2→42.144 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2484 1993 4.14 %
Rwork0.2069 --
obs0.2086 48166 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→42.144 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6646 0 85 215 6946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046918
X-RAY DIFFRACTIONf_angle_d0.6239358
X-RAY DIFFRACTIONf_dihedral_angle_d10.0074305
X-RAY DIFFRACTIONf_chiral_restr0.0381061
X-RAY DIFFRACTIONf_plane_restr0.0041239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.31551370.30363175X-RAY DIFFRACTION96
2.255-2.3160.32561410.28143257X-RAY DIFFRACTION99
2.316-2.38420.29311420.26843301X-RAY DIFFRACTION99
2.3842-2.46110.32781410.25973252X-RAY DIFFRACTION99
2.4611-2.54910.27211410.25973270X-RAY DIFFRACTION99
2.5491-2.65110.29561430.25843316X-RAY DIFFRACTION100
2.6511-2.77170.31791410.25733268X-RAY DIFFRACTION100
2.7717-2.91780.26861430.25283300X-RAY DIFFRACTION100
2.9178-3.10060.28181430.22693290X-RAY DIFFRACTION99
3.1006-3.33990.23371410.21733284X-RAY DIFFRACTION98
3.3399-3.67580.25671440.1943312X-RAY DIFFRACTION100
3.6758-4.20730.20631440.17163349X-RAY DIFFRACTION99
4.2073-5.29910.21691460.15633348X-RAY DIFFRACTION99
5.2991-42.15180.22831460.19473451X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.18480.50630.47372.7846-0.17993.43720.0264-0.0020.0972-0.1039-0.1590.11380.0005-0.0318-0.00620.27890.0244-0.00370.2323-0.02610.27423.39283.95914.3988
22.37960.3728-0.87551.2689-0.00662.00780.0496-0.36390.09990.4590.07980.3362-0.193-0.87270.00030.60.02070.15320.97290.05950.5099-8.37763.771249.8385
33.4617-0.16940.02643.8483-0.32813.27660.1633-0.19810.06150.4435-0.3093-0.431-0.04250.2944-0.0220.4009-0.0757-0.09350.35620.0680.375530.81744.350447.8901
41.686-0.6087-0.02131.11390.04890.6266-0.15670.9656-0.0079-0.79840.3297-0.73510.45010.93810.02040.78310.09410.20651.4385-0.14240.914642.942-2.382213.1781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 54 through 302)
2X-RAY DIFFRACTION2chain 'A' and (resid 303 through 479 )
3X-RAY DIFFRACTION3chain 'B' and (resid 54 through 302 )
4X-RAY DIFFRACTION4chain 'B' and (resid 303 through 478)

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